The area around Canajoharie was all wilderness until the Palatine Germans began settling in the general area starting in the 1720s. The Palatines who settled near present day Canajoharie, however, settled mainly in Stone Arabia, and the present day village was very sparsely populated until after the Revolution. The first church built in Canajoharie, the Union Church, built in 1818, was shared by various Protestant denominations, with all welcomed except Methodists and Universalists. In essence this meant the church was shared by the Lutheran and Reformed denominations that the Palatines favored. It would be more than ten years before there would be a pastor resident in Canajoharie.

The dedication sermon preached at the Union Church in 1818 was given by a Lutheran minister from Schoharie, Rev. George A. Lintner, and, while there was no resident minister, it is most likely that many of the visiting ministers were Lutheran and that services were held in German as well as English. Gradually the individual denominations organized and built their own churches; the Dutch Reformed formed a separate congregation and built their own church in 1927. The German speaking Lutherans formed St. John's Lutheran Church in 1935, and built their first church on the lot that now houses Bassett Healthcare in 1839. Meanwhile, the English speaking Lutherans continued to use the Union Church until 1839, when it was sold and moved to make way for the enlargement of the Erie Canal. The building was moved to the current location of St Mark's Lutheran, and exclusively served the newly formed St Mark's Lutheran congregation until 1870, when the current church was built. Canajoharie continued to have two separate Lutheran congregations until 1970, when they began sharing a pastor. The two churches were formally merged in 1975, and the St. John's building on Montgomery St. sold.

The earliest formally organized congregation in Canajoharie was the Dutch reformed, begun in 1827. The church had a resident pastor, at first shared with a Reformed congregation in Sprakers, since that date. For more than ten years the congregation continued to use the Union Church. In 1836 the congregation began planning for their own building. The building was built on a lot on Front street, donated by Mr. John Frey. The building was completed in 1842. A 2,000 pound bell was purchased in 1859, and additions made to the building in that year, and again in 1870, 1891 and 1925. The original construction date of the existing church of 1842 makes the Reformed Church the oldest existing church building in Canajoharie, although many of the rural churches were organized and constructed earlier. The church continues to be active in community affairs, and was recently renovated.

Methodism first came to the area in 1809, and services have been held with some regularity since 1828, when Palatine Bridge was added to the Herkimer circuit of traveling preachers.

In those early days services were held when the preacher arrived, usually once every two weeks. Services were held in schoolhouses or in homes. A few years later, in 1830, the local Methodist Church was officially incorporated. After several years of meeting in a wagon shop the congregation built their first church in the 1830s. The Methodists were the first denomination in the village to have their own church, a circumstance that is no doubt related to the fact that they were not allowed to use the existing Union Church. This first Methodist Church was located on the eastern side of Palatine Bridge. A few years later, in 1842, the Methodists built a stone church on the site of the present church on East Main St. This structure was one story, with the church auditorium the only room. The church was expanded, and a second story added, in the 1860s. In January, 1915, on a sub-zero night, the original Methodist Church burned. Firemen fought the fire from the 4th floor Beech-Nut gum building and from the roof of the business block on Church St. The congregation rebuilt on the same site. The current church was dedicated on May 28, 1916.

Some of the earliest churches in the Mohawk Valley were Anglican churches, the Church or England, England holding political sway over the region for most of the colonial period. However, after the revolution, when many of English descent migrated to Canada, the only Episcopalian church left in the county was St. Ann's in Amsterdam. But, by the middle 1800s additional immigration and the return of some loyalist descendants from Canada engendered the need for a new Episcopal congregation in Canajoharie, called St. Polycarp's Mission. The congregation held services sporadically, subject to the availability of a priest, over the next 20 years. These services were generally held in the Lutheran or Methodist churches of the village. In 1873 Dr. Joseph White organized the building of the present church, which was re-named the Episcopal Church of the Good Shepherd. The building was completed in 1874. Services continued to be sporadic, however, as a minister, when one was available at all, was usually shared with other area Episcopalian congregations in neighboring villages. It would be 50 years before the church had regular Sunday services. Membership rose toward the middle of the 20th century, and the basement was excavated to make room for Sunday school classes. The Good Shepherd absorbed Fort Plain's Holy Cross Episcopal in the 1980s, and now shares a pastor with Cherry Valley.

Although the first Christian presence in the Mohawk Valley was that of the French Jesuits, there were no Catholic churches until large numbers of Catholic immigrants began coming to the area in the mid 1800s. In 1862 a congregation was formed in Canajoharie, with a church constructed on the corner of Cliff and Walnut Streets, with the basement carved from the limestone bedrock, and the the stone for the church quarried on or near the property. In those early years a priest traveled from Cooperstown. Church membership grew rapidly, and St. Peter and Paul had its own resident priest by the 1870s, and spawned missions in Fort Plain and St. Johnsville in the 1880's. The building was rebuilt in the 1890s. In 2009 the church closed to merge with thier Fort Plain site to become Our Lady of Hope Church.This exhibit was made possible in part by a Parent and Child Library Services grant from the New York State Library, New York State Education Department.Much of the information in this exhibit was provided by the book "Steeple Chase: A History of the Churches in the Town of Canajoharie, Montgomery County, NY" published by the Montgomery County Department of History and Archives